 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jan 30, 2023 |
| Title |
Mouse |
| Sample type |
SRA |
| |
|
| Source name |
Mouse_splenocytes
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Splenocytes
strain: C57BL/6J
|
| Treatment protocol |
Splenocytes were sorted from the spleens of seven vertebrate species
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Spleen tissues were processed with the flat end of a syringe in a 100 mm culture dish containing 5 ml cold FACS buffer (2% FBS in PBS), then passed through a 70 μm cell strainer into a 15 ml tube. Cells were centrifuged to remove the supernatant. Cell pellets were treated with 1ml ACK (Ammonium-Chloride-Potassium) Lysing Buffer to remove the red blood cells. After washing with 10 ml cold FACS buffer, the remaining cells were stained with 7AAD (Part 76332; Lot B226294 Biolegend) for 30 min at 4 °C, then washed and resuspended in cold FACS buffer for flow cytometric sorting using FACS Aria II Cell Sorter (BD Biosciences). Sorted 7AAD- cells with a viability higher than 90% were used for 10X genomics scRNA-seq. Finally, libraries were sequenced on a NovaSeq 6000 system with NovaSeq 6000 S4 Reagent Kit (300 cycles).
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
The 10x Genomics Cell Ranger (3.0.1 version) pipeline was used to demultiplex raw files into FASTQ files, extract barcodes and UMI, filter, and map reads to the corresponding reference genome, and generate a matrix containing UMI counts.
A 10x Genomics Cell Ranger pipeline was used to identify clonotypes by alignment and annotation with the default settings.
Genome_build: Fish:GRCz11, Frog:Xenopus_laevis_v2, Mouse:GRCm38, Rat:Rnor_6.0, Pig:Sscrofa11, Monkey:Mmul_8, Human:GRCh38
Supplementary_files_format_and_content: Supplementary_files_format_and_content: filtered_feature_bc_matrix.tar contains counts matrix (stored in the Market Exchange Format for sparse matrices).
|
| |
|
| Submission date |
Oct 19, 2021 |
| Last update date |
Jan 30, 2023 |
| Contact name |
Cangang Zhang |
| E-mail(s) |
cg.zhang20195028@stu.xjtu.edu.cn
|
| Phone |
13636810556
|
| Organization name |
xian jiaotong university
|
| Street address |
Yanta district, xi 'an city, shaanxi province
|
| City |
xian |
| State/province |
State... |
| ZIP/Postal code |
710000 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE186158 |
Single-cell transcriptomic atlas reveals the evolution of immune cells and molecules across multiple vertebrate species |
|
| Relations |
| BioSample |
SAMN22415780 |
| SRA |
SRX12693842 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5639494_Mouse.tar.gz |
73.4 Mb |
(ftp)(http) |
TAR |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
